The study suggests eight fish stocks will not present an increase in fishing opportunities, with ministers also saying shares in five-and-a-half years’ time will still be less than their current equivalent.
Currently, the average UK landing percentage of total EU and UK quota combined for North Sea cod is 63.5 per cent.
However, the analysis says this will drop to 57 per cent – the maximum percentage of total EU and UK quota available to the UK – under the Brexit deal.
Similar decreases have been estimated for North Sea haddock (92.5 per cent to 84.2 per cent), Rockall haddock (88.4 per cent to 85 per cent), North Sea saithe (31.6 per cent to 26 per cent), North Sea whiting (82.7 per cent to 73.5 per cent) and North Sea hake (55.6 per cent to 53.6 per cent).
The figures remain the same both before and after the deal for Rockall cod (75 per cent) and West of Scotland cod (81.2 per cent).
Rural economy secretary Fergus Ewing said the analysis was “deeply troubling”.
He said: “Scottish coastal communities were told that any Brexit deal would mean a very large rise in fishing opportunities.
“In fact, for the key stocks that the Scottish industry depends on, far from seeing a big increase, there will actually be a fall in the quantity of fish they can land.
“We were also told that a red line for the UK Government was that the fisheries deal would not be tied to the overall trade deal.
“In fact, fisheries is hardwired into the overall deal, meaning any attempt to reduce EU access in future will lead to trade sanctions – hitting key Scottish industries like salmon producers.
“This is a terrible outcome for Scotland’s coastal communities. The small gains in quota for mackerel and herring are far outweighed by the impact of losses of haddock, cod and saithe – and that threatens to harm onshore jobs and businesses too, linked to harbours, fish markets and processing facilities.
“As our analysis shows, there is very little here to celebrate.”
While there is no increase for North Sea or Rockall haddock, other haddock quotas will rise including Irish Sea (54.2 per cent to 56 per cent) West of Scotland (77.3 per cent to 80.6 per cent) and Celtic Sea (8.8 per cent to 20 per cent).
Other increased fishing opportunities will be available for West of Scotland saithe (47.1 per cent to 51 per cent) and West of Scotland whiting (58.7 per cent to 65.9 per cent).
First Minister Nicola Sturgeon tweeted her criticisms, saying: “A better deal for fishing is the only Brexit justification the Tories have ever been able to offer Scotland.
“This analysis shows just how spectacularly they’ve broken that promise. For some key stocks the deal actually delivers a worse outcome than the (Common Fisheries Policy).”
Mike Park, Scottish White Fish Producers Association (SWFPA) chief executive, also said: “Setting politics aside, the members of SWFPA are deeply aggrieved at the very challenging situation they now face for 2021."
A UK Government spokesperson said: “The UK and the EU have agreed an historic Fisheries Framework Agreement that reflects the UK’s new status as an independent coastal state, and works to protect and promote the rights of fishermen across the UK.
“By regaining control of our waters, This deal puts us in a position to rebuild our fishing fleet and deliver increased fishing quotas through annual negotiations with the EU and other coastal states. In the first year this will result in an immediate uplift of 15 per cent, before annual negotiations.
“Scotland, like the rest of the UK, will benefit from tariff-free access to EU markets and investment in our fishing communities as we free ourselves from the EU’s Common Fisheries Policy.”
Labour leader Sir Keir Starmer was meanwhile facing a high-profile revolt over his decision to back Boris Johnson's EU trade deal in this week's Commons vote.
Former shadow chancellor John McDonnell and ex-cabinet minister Ben Bradshaw are among the signatories to a statement calling on opposition parties not to support the "rotten" agreement.
Sir Keir has said he would call on Labour MPs to support the "thin" post-Brexit free trade agreement, despite concerns that it will fail to protect many key economic sectors.
He argued that the alternative of ending the Brexit transition period on December 31 without a deal in place would be even worse for the economy.
However, his stance has upset some pro-Europeans in his party, who say they should not support a flawed agreement and should abstain instead.
The statement has been organised by Another Europe Is Possible and Labour For A Socialist Europe - both on the left - but has attracted support from both wings of the party.
As well as Mr Bradshaw, signatories include ex-cabinet minister Lord Adonis from the Blairite wing of the party.
From the left, Mr McDonnell is joined another former shadow cabinet minister Clive Lewis.
The statement warns that it is the duty of the opposition to provide proper parliamentary scrutiny and to set out an alternative.
"That task gets harder if opposition parties fall into the trap of rallying around this rotten deal," the statement said.
Other signatories are said to include former MEPs, councillors and local activists.Labour is alone among the opposition parties in saying it will support the deal - with the SNP and the Liberal Democrats having said they will vote against it.The DUP, which backed Brexit, has also said it will oppose the deal because the Brexit divorce settlement imposes customs checks between Northern Ireland and the rest of the UK.